New cooling system, still overheating.

I will pickup a infrared thermometer and grab some readings.

Any idea where I should take my readings?

Basically all over.
Radiator hose, both upper and lower.
Radiator in different spots.
Water pump.
Intake.
Thermostat housing.
Engine block and heads in different spots.

What you are looking for is how much variation there is. Say the intake is really hot and the upper radiator hose is, really cool then the thermostat would be worth checking out.